Imaging-based data can be interpreted as a point pattern either via the transcript locations or via cell centroids. Alternatively, the segmented cellular outlines can be interpreted as an irregular lattice. High throughput (HTS)-based approaches are most often recorded on a regular lattice. This enables either point pattern or lattice data analysis (Baddeley, Rubak, and Turner 2015; Pebesma and Bivand 2023; Rao et al. 2021). Data: (Shi et al. 2023; 10X 2022)..

This vignette provides an overview of exploratory data analysis techniques tailored to the data modalities arising from the two primary spatial transcriptomic technologies: image-based methods (e.g., MERFISH, CosMx, Xenium) and spot-based approaches (e.g., Visium).

Image-based techniques yield subcellular-resolution images, allowing for the study of cells within their natural context. This data can be analysed as spatial point pattern where the points represent cells. Alternatively, we can rely on the segmentation of each individual cell and interpret the collection of all cells as an irregular lattice.

In contrast, spot-based methods, not yet achieving subcellular resolution, produce data represented as a regularly spaced grid corresponding to the sampling locations (spots). Each location has the same area and consists of a collection of different measurements.

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References

10X. 2022. “Mouse Brain Section (Coronal).” https://www.10xgenomics.com/datasets/mouse-brain-section-coronal-1-standard.
Baddeley, Adrian, Ege Rubak, and Rolf Turner. 2015. Spatial Point Patterns. 1st ed. CRC Interdisciplinary Statistics Series. CRC Press, Taylor & Francis Group.
Pebesma, Edzer, and Roger Bivand. 2023. Spatial Data Science: With Applications in R. 1st ed. New York: Chapman and Hall/CRC. https://doi.org/10.1201/9780429459016.
Rao, Anjali, Dalia Barkley, Gustavo S. França, and Itai Yanai. 2021. “Exploring Tissue Architecture Using Spatial Transcriptomics.” Nature 596 (7871): 211–20. https://doi.org/10.1038/s41586-021-03634-9.
Shi, Hailing, Yichun He, Yiming Zhou, Jiahao Huang, Kamal Maher, Brandon Wang, Zefang Tang, et al. 2023. “Spatial Atlas of the Mouse Central Nervous System at Molecular Resolution.” Nature 622 (7983): 552–61.